Roots of angiosperm formins: The evolutionary history of plant FH2 domain-containing proteins

Additional file 1:

Summary of FH2 proteins analyzed in this study (MG_A1.xls). Full list of taxa and FH2 protein sequences included in this study, including an overview of protein domain structure. Database source and accession code is included for every sequence (for database abbreviations see Materials and Methods). For cases where gene structure prediction has been modified, newly predicted protein sequences are provided in Additional file 2. For abbreviations and SMART or Pfam identifiers of additional conserved domains found in the predicted proteins see legends to Tables 1 and 2 and Additional files 4 and 5; sp – signal peptide, tm – transmembrane domain; NA – not available (usually due to incomplete sequence). Format: MS Excel (*.xls).

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Additional file 2:

Predicted protein sequences of selected formins (MG_A2.txt). Protein sequences corresponding to genes listed in Additional file 1 whose prediction has been modified compared to the original database versions. Format: FASTA, raw text (*.txt).

Format: TXT Size: 93KB Download file

Additional file 3:

Phylogenetic tree of the FH2 domains (MG_A3.pdf). An unrooted maximum likelihood tree constructed as described in Materials and Methods. For a full list of list of genes, see Additional file 1. Numbers at nodes denote bootstrap values (out of 500 replicates; branches supported in all bootstraps marked by a dot). For comparison, bootstrap values from a NJ tree constructed on the basis of the same data are shown in green for major branches (from 100 bootstrap samples). Format: Adobe portable document (*.pdf).

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Additional file 4:

Diversity and domain structure of non-plant FH2 proteins (MG_A4.pdf). For each species, total number of FH2 domain-containing proteins (formins) is given, together with numbers of formins carrying any of the additional listed domains or motifs. Complete and draft genomes are shown in bold. For abbreviations and database accessions of domains found in more than one species see legend to Tab.1; domains found only in a single species (denoted as "other") are: DEP – domain found in Dishevelled, Egl-10, and Pleckstrin [Smart: SM00049], ZnF – zinc finger [Smart: SM00355], PHD – PHD Zinc Finger [Smart: SM00249], HDAC_int – histone deacetylase interacting domain [Smart: SM00761], BROMO [Smart: SM00297], C1 [Smart: SM00109], FHA – Forkhead-associated [Smart: SM00240], TPR – tetratricopeptide repeats [Smart: SM00028], ARM – Armadillo/beta-catenin repeats [Smart: SM00185], 1i84 – contractile protein [PDB: 1i84], KISc – kinesin motor [Smart: SM00129], SAP [Smart: SM00513], FYVE [Smart: SM00064], PAN_1 [Pfam: PAN_1], WW – a conserved domain containing two tryptophan residues [Smart: SM00456]. For commonly appearing domains, the table is color-coded as follows: green – present in all formins of the species, yellow – present in some formins, orange – absent, grey – incomplete data. Format: Adobe portable document (*.pdf).

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Additional file 5:

Diversity and domain structure of plant FH2 proteins (MG_A5.pdf). For each species, the total number of complete formin sequences is given as FH2, and the number of incomplete sequences that did not allow conclusive analysis of domain architecture is as FH2 (partial). Class I, Class II, Class III and Other FH2 denote numbers of formins carrying FH2 domains from the respective clades (or unassigned ones); the remaining abbreviations denote additional domains and motifs found in plant formins: Sec10 – Exocyst complex component Sec10 [Pfam: Sec10]; for remaining domain abbreviations and database accessions see legend to Table 1 and Table 2. Complete and draft genomes are shown in bold. For commonly appearing domains, the table is color-coded as follows: green – present in all formins of the species (for FH1) or of all characterized formins of the corresponding class (for remaining domains in color), yellow – present in some formins, blue – present in a formin that cannot be assigned to the corresponding class, orange – absent, grey – incomplete data. Format: Adobe portable document (*.pdf).

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Additional file 6:

Model of the RhoGAP-related domain from Phypa7 (MG_Phypa7.pdb). Coordinates of the model in the PDB format (*. pdb) which can be viewed using e.g. the free Deep View Viewer [110].

Format: PDB Size: 95KB Download file

Additional file 7:

Summary of PTEN domains analyzed in this study (MG_A7.xls). List of taxa and PTEN protein sequences included in this study, in addition to FH2 – containing sequences that are listed in Additional file 1. Database source and accession code is included for every sequence; for database source abbreviations see legend to Additional file 1. For abbreviations and SMART or Pfam identifiers of additional conserved domains found in the predicted proteins see legends to Tables 1 and 2 and Additional files 1, 4 and 5; additional domains are: ABC-tran – ATP-binding casette transporter [Pfam:PF00005], MYSc – myosin/large ATPase [Smart: SM00242], SH2 – Src homology 2 domain [Smart: SM00252], PTB – phosphotyrosine-binding domain [Smart: SM00462], LIM – Zinc-binding domain present in Lin-11, Isl-1 and Mec-3 [Smart: SM00132]. For cases where gene structure prediction has been modified, new predicted protein sequences are provided in Additional file 8. Format: MS Excel (*.xls).

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Additional file 8:

Predicted protein sequences of selected PTEN-containing proteins (MG_A8.txt). Modified protein sequence predictions corresponding to some of the genes listed in Additional file 7. Format: FASTA, raw text (*.txt).

Format: TXT Size: 5KB Download file

Additional file 9:

Phylogenetic tree of 90 PTEN domains (MG_A9.pdf). An unrooted maximum likelihood tree of 90 PTEN domains constructed as described in Materials and Methods. For a full list of list of genes, see Additional file 7. Note that this tree is based on more sequences but a shorter alignment than that from Figure 3. For the 5 PTEN sequences not represented in any of the trees (Figure 3 or Additional file 9) due to close relationship to another PTEN or identification only during the final database checks, closest relatives are shown in Additional file 7. Numbers at nodes denote bootstrap values (out of 500 replicates; branches supported in all bootstraps marked by a dot). For comparison, bootstrap values from a NJ tree constructed on the basis of the same data are shown in green for major branches (from 500 bootstrap samples). Format: Adobe portable document (*.pdf).

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